Hi Brad
I did not restart the master CloudMan node.
I only restarted the services (Galaxy, PostgreSQL and SGE).
I do not have these problems without creating the logical volume.
Kind Regards
Yves
Yves;
I'm hoping Enis can jump in here since he is more familiar with the
internals of CloudMan an
On Wed, Feb 15, 2012 at 6:07 PM, Dannon Baker wrote:
>
> Main still runs these jobs in the standard non-split fashion, and as a
> resource that is occasionally saturated (and thus doesn't necessarily have
> extra resources to parallelize to) will probably continue doing so as long
> as there's sig
On Feb 16, 2012, at 5:15 AM, Peter Cock wrote:
> On Wed, Feb 15, 2012 at 6:07 PM, Dannon Baker wrote:
>>
>> Main still runs these jobs in the standard non-split fashion, and as a
>> resource that is occasionally saturated (and thus doesn't necessarily have
>> extra resources to parallelize to)
On Wed, Feb 15, 2012 at 6:07 PM, Dannon Baker wrote:
> Good luck, let me know how it goes, and again - contributions are certainly
> welcome :)
I think I found the first bug, method split in lib/galaxy/datatypes/sequence.py
for class Sequence assumes four lines per sequence. This would make
sense
On Thu, Feb 16, 2012 at 10:47 AM, Peter Cock wrote:
> On Wed, Feb 15, 2012 at 6:07 PM, Dannon Baker wrote:
>> Good luck, let me know how it goes, and again - contributions are certainly
>> welcome :)
>
> I think I found the first bug, method split in
> lib/galaxy/datatypes/sequence.py
> for clas
On Feb 16, 2012, at 4:47 AM, Peter Cock wrote:
> On Wed, Feb 15, 2012 at 6:07 PM, Dannon Baker wrote:
>> Good luck, let me know how it goes, and again - contributions are certainly
>> welcome :)
>
> I think I found the first bug, method split in
> lib/galaxy/datatypes/sequence.py
> for class Se
On Thu, Feb 16, 2012 at 1:53 PM, Fields, Christopher J
wrote:
>
> Makes sense from my perspective; splits have to be defined based on
> data type. It could be as low-level as defining a simple iterator per
> record, then a wrapper that allows a specific chunk-size. The split
> file creation coul
Hello,
I want to develop a galaxy wrapper for a tool that outputs an html
report (with images inside specific subfolders).
Do I need to do like the FastQC galaxy wrapper that reconstructs the
html so that they are all in the same folder?
Or is there a way to circumvent this so that I can keep the
Hi Dan,
I think I need a little more advice - what is the role of the script
scripts/extract_dataset_part.py and the JSON files created
when splitting FASTQ files in lib/galaxy/datatypes/sequence.py,
and then used by the class' process_split_file method?
Why is there no JSON file created by the b
On Thu, Feb 16, 2012 at 4:28 PM, Peter Cock wrote:
> Hi Dan,
>
> I think I need a little more advice - what is the role of the script
> scripts/extract_dataset_part.py and the JSON files created
> when splitting FASTQ files in lib/galaxy/datatypes/sequence.py,
> and then used by the class' process
Very cool, I'll check it out! The addition of the JSON files is indeed very
new and was likely unfinished with respect to the base splitter.
-Dannon
On Feb 16, 2012, at 1:24 PM, Peter Cock wrote:
> On Thu, Feb 16, 2012 at 4:28 PM, Peter Cock wrote:
>> Hi Dan,
>>
>> I think I need a little mo
On Feb 16, 2012, at 12:24 PM, Peter Cock wrote:
> On Thu, Feb 16, 2012 at 4:28 PM, Peter Cock wrote:
>> Hi Dan,
>>
>> I think I need a little more advice - what is the role of the script
>> scripts/extract_dataset_part.py and the JSON files created
>> when splitting FASTQ files in lib/galaxy/dat
Hi All,
What is the recommend process for expanding the galaxyTool volume for an
existing galaxy instance (using EC2/cloudman)?
I tried the following, but it didnt' work for me.
0) Terminate cluster.
1) Amazon EC2- create snapshot of current galaxyTools volume
2) Amazon EC2- create volume from
On Thu, Feb 16, 2012 at 6:42 PM, Fields, Christopher J
wrote:
> On Feb 16, 2012, at 12:24 PM, Peter Cock wrote:
>> I've checked in my FASTA splitting, which now seems to be
>> working OK with my BLAST tests.
(If this was unclear, I mean checked into my branch - I don't
have commit privileges to t
Hi Dave,
Are you trying to modify the size of the tools volume for a cluster that's
been around for a while and you customized already or could this be a new
cluster?
The reason I'm asking is because as of Tuesday (3 days ago), the default
tools volume for any new cluster will be 10GB (vs 2GB previ
Hi Enis,
I installed a new test cluster earlier today and did notice that the new
clusters magically now have galaxyTool volumes with 10GB. That is a good
change.
However, you are correct. I have an existing cluster (that had the old 2 GB
volume size) that I'm trying to expand. With additional to
No problem; this should get you there:
1. With CloudMan running, go to the Admin console and stop Galaxy and
PostgreSQL services (in that order)
2. From instance's CLI: sudo umount /mnt/galaxyTools
3. From the AWS console, detach the tools volume (but remember as which
device it was attached)
4.
Hi all,
I configured Sample Tracking System in Galaxy to transfer datasets from a
sequencer to data libraries, however, after I selected the datasets to be
transferred on the sequencer and clicked "Transfer" button, the transfer
status has been "in queue" forever.
I didn't find any error message
Hi all,
I am having trouble producing HTML output with images. In the past I
have been able to produce HTML files with no images and it seemed to
work fine. However, now I am writing a script that produces
diagnostic images and I want to display all of the images on one page
using HTML. I am us
Well, I guess I figured it out... it turns out that galaxy does some
internal magic to automatically add the path of the output directory
to the filename when it is rendering the html. So what I needed to do
was to create the file in the temporary job directory and then just
use the file name with
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